The invention discloses a pellet type omeprazole enteric capsule and a preparation method thereof. The pellet type omeprazole enteric capsule is a sustained-release preparation, and is composed of a capsule shell and evenly mixed omeprazole pellets received in the capsule shell; each omeprazole pellet is composed of a blank pill core, a main drug layer, an isolation layer and an enteric layer in order from inside to outside, wherein the weight of the main drug layer accounts for 15-60% of that of the blank pill core, the weight of the isolation layer accounts for 10% of the total weight of the blank pill core and the main drug layer, the weight of the enteric layer accounts for 28-32% of the total weight of the blank pill core, the main drug layer and the isolation layer; besides, the enteric layers of 40-60% of omeprazole pellets are further coated with pigment layers; the weight of the pigment layer accounts for 0.5-1% of the total weight of the blank pill core, the main drug layer, the isolation layer and the enteric layer; the diameters of the blank pill cores are 0.8-1.0mm; the granularity of the omeprazole pellets is 14-20 meshes; each capsule contains 15-30mg of omeprazole. The pellet type omeprazole enteric capsule has the advantages of good acid resistance, sufficient active ingredient release without delay, good stability and the like.